TABLE 1.

List of genes gained/lost among geographic and phylogenetic PD-causing groups

Category	Annotationa
Genes absent from the Taiwan population (found in the contiguous U.S.)	Site-specific DNA-methyltransferase (QIS25725.1); ko K00571, ko K00590, ko K07319 (adenine-specific DNA-methyltransferase); PF01555
	Hypothetical protein (QIS26419.1)
	Peptidoglycan DD-metalloendopeptidase family protein (QIS26766.1); PF06594, PF00353 (RTX calcium-binding nonapeptide repeat)
	Site-specific DNA-methyltransferase (QIS25737.1); ko K00571, ko K00590, ko K07319 (adenine-specific DNA-methyltransferase); PF01555
	Pseudogene
Genes absent from the Spanish population (found in the contiguous U.S.)	CPD*: LacZ, beta-galactosidase/beta-glucuronidase; ko K01192 (beta-mannosidase)
	Glutamate 5-kinase (AAO28181.1); ko K00931; PF00696
PD-II and PD-III exclusive genes in the California population	Alpha/beta fold hydrolase (QIS25057.1); ko K02170, ko K07002 (pimeloyl-[acyl-carrier protein] methyl ester esterase)
	Hypothetical protein (QJP55224.1); PF04014 (antidote-toxin recognition MazE, bacterial antitoxin)
	Hypothetical protein (AAO28982.1)
PD-I and PD-III exclusive genes in the Southeast population excluding the Taiwanese clade	Hypothetical protein (QIS26118.1)
	Phage head morphogenesis protein (QIS26295.1); PF04233
Genes gained after introduction into Taiwan	CPD*: OM_channels Superfamily, Porin superfamily
	CPD*: DUF769 superfamily; ko K15125 (filamentous hemagglutinin)
	CPD*: entero_EhxA superfamily
	Hypothetical protein (QIS25070.1); RTX toxin (QIS25071.1)
Genes gained after introduction into Spain	Pseudogene: glycoside hydrolase family 125 protein; ko K09704 (uncharacterized protein); PF06824 (Metal-independent alpha-mannosidase)
	DUF596 domain-containing protein (QIS26773.1); PF04591
	Hypothetical protein (QID15519.1); hemagglutinin (QID15518.1); ko K02014 (iron complex outer membrane receptor protein)

^ako, KEGG orthology; PF, Pfam database entry ID; CPD*, conserved protein domain.